|
| Status |
Public on Jun 13, 2024 |
| Title |
HEK293T_RBFOX_STAMP |
| Sample type |
SRA |
| |
|
| Source name |
Kidney
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: Kidney
cell line: HEK293XT
cell type: immortalized cell line
replicate: 2
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Direct-zol RNA Miniprep Kits, Zymo Research (Cat # R2052)
PacBio Iso-seq SMRTbell prep kit 3.0 (PN: 102-396-000)
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Sequel II |
| |
|
| Description |
Long-read in situ RBFOX2-APOBEC1 STAMP
|
| Data processing |
Demultiplex primers with lima (v2.6.0)
Refine reads with Isoseq3 refine (v3.8.0)
Align reads using pbmm2 (v1.9.0)
Cluster reads with isoseq3 cluster (v3.8.0)
Filter for primary mapped reads with custom script
Identify gene editing using custom script
remove edits found in annotated SNP positions using custom script
Assembly: hg38
Supplementary files format and content: isoforms from clustering (.gff)
Supplementary files format and content: gene edits (.bed)
|
| |
|
| Submission date |
Aug 08, 2023 |
| Last update date |
Jun 13, 2024 |
| Contact name |
Brian Yee |
| E-mail(s) |
brian.alan.yee@gmail.com
|
| Organization name |
UCSD
|
| Department |
Health
|
| Lab |
Yeo
|
| Street address |
9500 Gilman Dr
|
| City |
La Jolla |
| State/province |
CA |
| ZIP/Postal code |
92093 |
| Country |
USA |
| |
|
| Platform ID |
GPL28352 |
| Series (2) |
| GSE240325 |
An in situ method for identification of transcriptome-wide protein-RNA interactions in cells [in_situ_STAMP - Long-Read]" |
| GSE240326 |
An in situ method for identification of transcriptome-wide protein-RNA interactions in cells |
|
| Relations |
| BioSample |
SAMN36887271 |
| SRA |
SRX21296349 |
